HEADER TRANSFERASE 14-MAR-18 6CQ7 TITLE THE SH3 DOMAIN OF MLK3 IN COMPLEX WITH POLY-PROLINE PEPTIDE DERIVED TITLE 2 FROM HTT COMPND MOL_ID: 1; COMPND 2 MOLECULE: MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 11, COMPND 3 HUNTINGTIN FUSION PROTEIN; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: MIXED LINEAGE KINASE 3,SRC-HOMOLOGY 3 DOMAIN-CONTAINING COMPND 6 PROLINE-RICH KINASE,MIXED LINEAGE KINASE 3,SRC-HOMOLOGY 3 DOMAIN- COMPND 7 CONTAINING PROLINE-RICH KINASE,HUNTINGTON DISEASE PROTEIN,HD PROTEIN; COMPND 8 EC: 2.7.11.25; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MAP3K11, MLK3, PTK1, SPRK, HTT, HD, IT15; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HUNTINGTON, PEPTIDE FUSION, MIXED LINEAGE KINASE 3, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.L.KALL,A.LAVIE REVDAT 3 04-OCT-23 6CQ7 1 REMARK REVDAT 2 11-DEC-19 6CQ7 1 REMARK REVDAT 1 19-SEP-18 6CQ7 0 JRNL AUTH S.L.KALL,A.LAVIE JRNL TITL THE SH3 DOMAIN OF MLK3 IN COMPLEX WITH POLY-PROLINE PEPTIDE JRNL TITL 2 DERIVED FROM HTT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0189 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 9765 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 544 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 678 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.72 REMARK 3 BIN R VALUE (WORKING SET) : 0.3860 REMARK 3 BIN FREE R VALUE SET COUNT : 40 REMARK 3 BIN FREE R VALUE : 0.3880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 542 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 30 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 60.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.73000 REMARK 3 B22 (A**2) : 1.73000 REMARK 3 B33 (A**2) : -3.45000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.114 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.132 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.123 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.035 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 579 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 511 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 795 ; 1.751 ; 1.957 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1188 ; 0.983 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 76 ; 6.313 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 27 ;34.665 ;23.704 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 75 ;13.066 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;17.108 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 78 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 685 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 124 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 301 ; 4.923 ; 5.862 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 300 ; 4.926 ; 5.833 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 378 ; 6.563 ; 8.702 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 379 ; 6.555 ; 8.737 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 278 ; 6.020 ; 6.292 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 276 ; 6.014 ; 6.229 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 417 ; 8.814 ; 9.226 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 598 ;10.601 ;65.093 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 593 ;10.609 ;64.440 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6CQ7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1000233209. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-AUG-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97857 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10431 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 59.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.5600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.460 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 5K28 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5 M AMMONIUM SULPHATE 0.1 M SODIUM REMARK 280 CITRATE PH 5.6 1.1 M LITHIUM SULPHATE, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+1/4 REMARK 290 8555 -Y,-X,-Z+3/4 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.18000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 63.27000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 21.09000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 42.18000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 21.09000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 63.27000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 59.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -42.18000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 35 REMARK 465 SER A 36 REMARK 465 HIS A 37 REMARK 465 MET A 38 REMARK 465 TYR A 39 REMARK 465 ALA A 40 REMARK 465 GLU A 114 DBREF 6CQ7 A 39 106 UNP Q16584 M3K11_HUMAN 41 108 DBREF 6CQ7 A 107 114 PDB 6CQ7 6CQ7 107 114 SEQADV 6CQ7 GLY A 35 UNP Q16584 EXPRESSION TAG SEQADV 6CQ7 SER A 36 UNP Q16584 EXPRESSION TAG SEQADV 6CQ7 HIS A 37 UNP Q16584 EXPRESSION TAG SEQADV 6CQ7 MET A 38 UNP Q16584 EXPRESSION TAG SEQRES 1 A 80 GLY SER HIS MET TYR ALA ASN PRO VAL TRP THR ALA LEU SEQRES 2 A 80 PHE ASP TYR GLU PRO SER GLY GLN ASP GLU LEU ALA LEU SEQRES 3 A 80 ARG LYS GLY ASP ARG VAL GLU VAL LEU SER ARG ASP ALA SEQRES 4 A 80 ALA ILE SER GLY ASP GLU GLY TRP TRP ALA GLY GLN VAL SEQRES 5 A 80 GLY GLY GLN VAL GLY ILE PHE PRO SER ASN TYR VAL SER SEQRES 6 A 80 ARG GLY GLY GLY PRO PRO PRO PRO GLY PRO ALA VAL ALA SEQRES 7 A 80 GLU GLU FORMUL 2 HOH *30(H2 O) HELIX 1 AA1 ASP A 72 GLY A 77 1 6 SHEET 1 AA1 5 GLN A 89 PRO A 94 0 SHEET 2 AA1 5 TRP A 81 VAL A 86 -1 N GLY A 84 O GLY A 91 SHEET 3 AA1 5 ARG A 65 SER A 70 -1 N SER A 70 O ALA A 83 SHEET 4 AA1 5 VAL A 43 ALA A 46 -1 N TRP A 44 O VAL A 66 SHEET 5 AA1 5 VAL A 98 SER A 99 -1 O SER A 99 N THR A 45 CRYST1 59.000 59.000 84.360 90.00 90.00 90.00 P 43 2 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016949 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016949 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011854 0.00000